jo comments

Author: philouail

R/AllGenerics.R

@@ -417,15 +417,13 @@ setGeneric("chromPeakData<-", function(object, value)
 #' spectra for one chromatographic peak (or a `Spectra` of length 0 if no
 #' spectrum was found for the respective chromatographic peak).
 #'
-#' Parameters `addColumnsChromPeaks` allow the user to add specific metadata
+#' Parameters `chromPeakColumns` allow the user to add specific metadata
 #' columns from the chromatographic peaks (`chromPeaks`) to the returned
 #' spectra object. This can be useful to retain information such as retention
 #' time (`rt`), m/z (`mz`). The columns will be named as they is written in the
-#' `chromPeaks` object with a prefix that is defined by the parameter
-#' `addColumnsChromPeaksPrefix`. The *peak ID* (i.e., the row name of the
-#' peak in the `chromPeaks` matrix) is always added to the spectra object as
-#' metadata column `paste0(addColumnsChromPeaksPrefix,id)`, by default it will
-#' be `"chrom_peak_id"`.
+#' `chromPeaks` object with the prefix `"chrom_peak_"`. The *peak ID*
+#' (i.e., the row name of the peak in the `chromPeaks` matrix) is always added
+#' to the spectra object as a metadata column named `"chrom_peak_id"`.
 #'
 #' See also the *LC-MS/MS data analysis* vignette for more details and examples.
 #'
@@ -460,15 +458,10 @@ setGeneric("chromPeakData<-", function(object, value)
 #' @param return.type `character(1)` defining the type of result object that
 #'     should be returned.
 #'
-#' @param addColumnsChromPeaks `character` vector with the names of the columns
+#' @param chromPeakColumns `character` vector with the names of the columns
 #'    from `chromPeaks` that should be added to the returned spectra object.
 #'    The columns will be named as they are written in the `chromPeaks` object
-#'    with a prefix that is defined by the parameter
-#'    `addColumnsChromPeaksPrefix`. Defaults to `c("mz", "rt")`.
-#'
-#' @param addColumnsChromPeaksPrefix `character(1)` defining the prefix that
-#'    should be used for the columns from `chromPeaks` that are added to the
-#'    returned spectra object. Defaults to `"chrom_peak_"`.
+#'    with a prefix `"chrom_peak_"`. Defaults to `c("mz", "rt")`.
 #'
 #' @param BPPARAM parallel processing setup. Defaults to [bpparam()].
 #'
@@ -517,7 +510,7 @@ setGeneric("chromPeakData<-", function(object, value)
 #' ms2_sps <- chromPeakSpectra(dda)
 #' ms2_sps
 #'
-#' ## spectra variable *peak_id* contain the row names of the peaks in the
+#' ## spectra variable *chrom_peak_id* contain the row names of the peaks in the
 #' ## chromPeak matrix and allow thus to map chromatographic peaks to the
 #' ## returned MS2 spectra
 #' ms2_sps$chrom_peak_id
@@ -817,23 +810,20 @@ setGeneric("featureDefinitions<-", function(object, value)
 #' spectra per feature).
 #'
 #' The information from `featureDefinitions` for each feature can be included
-#' in the returned [Spectra()] object using the `addColumnsFeatures` parameter.
+#' in the returned [Spectra()] object using the `featureColumns` parameter.
 #' This is useful for retaining details such as the median retention time (`rtmed`)
 #' or median m/z (`mzmed`). The columns will retain their names as specified
-#' in the `featureDefinitions` object, prefixed by the value of the
-#' `addColumnsFeaturesPrefix` parameter. Additionally, the *feature ID*
-#' (i.e., the row name of the feature in the `featureDefinitions` data.frame)
-#' is always added as a metadata column with the name
-#' `paste0(addColumnsFeaturesPrefix, "id")`, which defaults to `"feature_id"`.
+#' in the `featureDefinitions` object, prefixed by `"feature_"`
+#' (e.g., `"feature_mzmed"`). Additionally, the *feature ID* (i.e., the row
+#' name of the feature in the `featureDefinitions` data.frame) is always added
+#' as a metadata column named `"feature_id"`.
 #'
 #' See also [chromPeakSpectra()], as it supports a similar parameter for
 #' including columns from the chromatographic peaks in the returned spectra object.
 #' These parameters can be used in combination to include information from both
 #' the chromatographic peaks and the features in the returned [Spectra()].
 #' The *peak ID* (i.e., the row name of the peak in the `chromPeaks` matrix)
-#' is added as a metadata column with the name
-#' `paste0(addColumnsChromPeaksPrefix, "id")`, which defaults to
-#' `"chrom_peak_id"`.
+#' is added as a metadata column named `"chrom_peak_id"`.
 #'
 #' @param object [XcmsExperiment] or [XCMSnExp] object with feature defitions.
 #'
@@ -846,15 +836,11 @@ setGeneric("featureDefinitions<-", function(object, value)
 #'     `featureDefinitions(x)`). This parameter overrides `skipFilled` and is
 #'     only supported for `return.type` being either `"Spectra"` or `"List"`.
 #'
-#' @param addColumnsFeatures `character` vector with the names of the columns
+#' @param featureColumns `character` vector with the names of the columns
 #'     from `featureDefinitions` that should be added to the returned spectra
 #'     object. The columns will be named as they are written in the
-#'    `featureDefinitions` object with a prefix that is defined by the parameter
-#'    `addColumnsFeaturesPrefix`. Defaults to `c("mzmed", "rtmed")`.
-#'
-#' @param addColumnsFeaturesPrefix `character(1)` defining the prefix that
-#'     should be used for the columns from `featureDefinitions` that are added
-#'     to the returned spectra object. Defaults to `"feature_"`.
+#'    `featureDefinitions` object with the prefix `"feature_`.
+#'     Defaults to `c("mzmed", "rtmed")`.
 #'
 #' @param ... additional arguments to be passed along to [chromPeakSpectra()],
 #'     such as `method`.
@@ -866,7 +852,7 @@ setGeneric("featureDefinitions<-", function(object, value)
 #' the order and the length matches parameter `features` (or if no `features`
 #' is defined the order of the features in `featureDefinitions(object)`).
 #'
-#' Spectra variables `"peak_id"` and `"feature_id"` define to which
+#' Spectra variables `"chrom_peak_id"` and `"feature_id"` define to which
 #' chromatographic peak or feature each individual spectrum is associated
 #' with.
 #'

R/XcmsExperiment-functions.R

@@ -794,8 +794,7 @@
                                    msLevel = 2L, expandRt = 0, expandMz = 0,
                                    ppm = 0, skipFilled = FALSE,
                                    peaks = integer(),
-                                   addColumnsChromPeaks = c("rt", "mz"),
-                                   addColumnsChromPeaksPrefix = "chrom_peak_",
+                                   chromPeakColumns = c("rt", "mz"),
                                    BPPARAM = bpparam()) {
     method <- match.arg(method)
     pks <- .chromPeaks(x)[, c("mz", "mzmin", "mzmax", "rt",
@@ -821,8 +820,7 @@
     res <- bpmapply(
         split.data.frame(pks, f),
         split(spectra(x), factor(fromFile(x), levels = levels(f))),
-        FUN = function(pk, sp, msLevel, method, addColumnsChromPeaks,
-                       addColumnsChromPeaksPrefix) {
+        FUN = function(pk, sp, msLevel, method, chromPeakColumns) {
             sp <- filterMsLevel(sp, msLevel)
             idx <- switch(
                 method,
@@ -833,17 +831,14 @@
                 largest_bpi = .spectra_index_list_largest_bpi(sp, pk, msLevel))
             ids <- rep(rownames(pk), lengths(idx))
             res <- sp[unlist(idx)]
-            pk_data <- as.data.frame(pk[ids, addColumnsChromPeaks,
-                                        drop = FALSE])
+            pk_data <- as.data.frame(pk[ids, chromPeakColumns, drop = FALSE])
             pk_data$id <- ids
-            colnames(pk_data) <- paste0(addColumnsChromPeaksPrefix,
-                                          colnames(pk_data))
+            colnames(pk_data) <- paste0("chrom_peak_", colnames(pk_data))
             res <- .add_spectra_data(res, pk_data)
             res
         },
         MoreArgs = list(msLevel = msLevel, method = method,
-                        addColumnsChromPeaks = addColumnsChromPeaks,
-                        addColumnsChromPeaksPrefix = addColumnsChromPeaksPrefix),
+                        chromPeakColumns = chromPeakColumns),
         BPPARAM = BPPARAM)
     Spectra:::.concatenate_spectra(res)
 }

R/XcmsExperiment.R

@@ -1229,8 +1229,7 @@ setMethod(
                                 "largest_tic", "largest_bpi"),
              msLevel = 2L, expandRt = 0, expandMz = 0, ppm = 0,
              skipFilled = FALSE, peaks = character(),
-             addColumnsChromPeaks = c("rt", "mz"),
-             addColumnsChromPeaksPrefix = "chrom_peak_",
+             chromPeakColumns = c("rt", "mz"),
              return.type = c("Spectra", "List"), BPPARAM = bpparam()) {
         if (hasAdjustedRtime(object))
             object <- applyAdjustedRtime(object)
@@ -1246,19 +1245,15 @@ setMethod(
         else pkidx <- integer()
         res <- .mse_spectra_for_peaks(object, method, msLevel, expandRt,
                                       expandMz, ppm, skipFilled, pkidx,
-                                      addColumnsChromPeaks,
-                                      addColumnsChromPeaksPrefix,
+                                      chromPeakColumns,
                                       BPPARAM)
         if (!length(pkidx))
             peaks <- rownames(.chromPeaks(object))
         else peaks <- rownames(.chromPeaks(object))[pkidx]
-        if (return.type == "Spectra") {
-            col <- paste0(addColumnsChromPeaksPrefix, "id")
-            res <- res[as.matrix(findMatches(peaks, res[[col]]))[, 2L]]
-        } else {
-            col <- paste0(addColumnsChromPeaksPrefix, "id")
-            as(split(res, factor(res[[col]], levels = peaks)), "List")
-        }
+        if (return.type == "Spectra")
+            res <- res[as.matrix(findMatches(peaks, res$chrom_peak_id))[, 2L]]
+        else
+            as(split(res, factor(res$chrom_peak_id, levels = peaks)), "List")
     })
 
 #' @rdname reconstructChromPeakSpectra
@@ -1781,9 +1776,7 @@ setMethod(
     function(object, msLevel = 2L, expandRt = 0, expandMz = 0, ppm = 0,
              skipFilled = FALSE, return.type = c("Spectra", "List"),
              features = character(),
-             addColumnsFeatures = c("rtmed", "mzmed"),
-             addColumnsFeaturesPrefix = "feature_",
-             addColumnsChromPeaksPrefix = "chrom_peak_",
+             featureColumns = c("rtmed", "mzmed"),
              ...) {
         return.type <- match.arg(return.type)
         if (!hasFeatures(object))
@@ -1803,17 +1796,16 @@ setMethod(
         sps <- .mse_spectra_for_peaks(
             object, msLevel = msLevel, expandRt = expandRt,
             expandMz = expandMz, ppm = ppm, skipFilled = skipFilled,
-            peaks = unique(pindex),
-            addColumnsChromPeaksPrefix = addColumnsChromPeaksPrefix, ...)
-        col <- paste0(addColumnsChromPeaksPrefix, "id")
+            peaks = unique(pindex), ...)
         mtch <- as.matrix(
-            findMatches(sps[[col]], rownames(.chromPeaks(object))[pindex]))
+            findMatches(sps$chrom_peak_id,
+                        rownames(.chromPeaks(object))[pindex]))
         sps <- sps[mtch[, 1L]]
         fid <- rep(
             ufeatures, lengths(featureDefinitions(object)$peakidx[findex]))
-        f_data <- featureDefinitions(object)[fid[mtch[, 2L]], addColumnsFeatures]
+        f_data <- featureDefinitions(object)[fid[mtch[, 2L]], featureColumns]
         f_data$id <- fid[mtch[, 2L]]
-        colnames(f_data) <- paste0(addColumnsFeaturesPrefix, colnames(f_data))
+        colnames(f_data) <- paste0("feature_", colnames(f_data))
         sps <- .add_spectra_data(sps, f_data)
         if (return.type == "List") {
             sps <- List(split(sps, f = factor(sps$feature_id,

man/chromPeakSpectra.Rd

@@ -206,7 +206,7 @@ dda_spectra$chrom_peak_id
 ```
 
 Some information about the chromatographic peak can also be added to the 
-returned `Spectra` object using the `addChromPeaksColumns` parameter in 
+returned `Spectra` object using the `chrompeakColumns` parameter in 
 `chromPeakSpectra()`. By default, the m/z and retention time of the 
 chromatographic peak are added to the spectra metadata.